Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Applying proteomics to the diagnosis and treatment of ALS and related diseases.

  PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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  Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

  csf spinal biofluid muscle 2d-dige antibody luminex

• Longitudinal analysis of early stage sarcopenia in aging rhesus monkeys.

  PMID 18983905 · PMC2693938 · Experimental gerontology · 2009 · 8 claims · 6 setups

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  mtDNA deletion mutations induce ETS enzyme abnormalities (COXneg/SDHhyp phenotypes) linked to intra-fiber atrophy and fiber loss

  rhesus vastus muscle single dual hematoxylin immunohistochemistry

• Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes.

  PMID 19833877 · PMC2797941 · Diabetes · 2010 · 7 claims · 5 setups

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  Mitochondrial protein abundance is decreased in insulin-resistant (obese and type 2 diabetic) skeletal muscle

  skeletal volunteers bsa shotgun euglycemic-hyperinsulinemic immunoblot

• Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

  PMID 31980607 · PMC6981202 · Nature communications · 2020 · 6 claims · 4 setups

  Has reproduction · 52

  A meta-analysis (MetaMEx) of 66 published human skeletal muscle datasets reveals pathways selectively activated by inactivity, aerobic versus resistance, and acute versus chronic exercise training.

  skeletal healthy transcriptomic qpcr metabolic

• Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.

  PMID 31825657 · PMC7099524 · American journal of physiology. Cell physiology · 2020 · 8 claims · 8 setups

  Has reproduction · 64

  L6, C2C12, and primary human myotubes show substantial heterogeneity in transcriptomic and metabolic profiles

  c2c12 transcriptomic proliferation brdu

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar).

  PMID 33158415 · PMC7648306 · Genetics, selection, evolution : GSE · 2020 · 7 claims · 5 setups

  Has reproduction · 85

  A QTL for pre-smolt growth was identified on chromosome 9.

  atlantic isotope snp rnaseq

• Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities.

  PMID 32695266 · PMC7352056 · Computational and structural biotechnology journal · 2020 · 8 claims · 8 setups

  Has reproduction · 78

  The majority of differentially expressed genes in PCOS are downregulated regardless of tissue type and phenotype

  lutein subcutaneous cumulus skeletal microarray pathway

• Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells.

  PMID 36093058 · PMC9459695 · iScience · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  PFA-perfusion-based isolation preserves the true in vivo chromatin accessibility state, avoiding artifacts caused by tissue dissociation-induced activation

  quiescent satellite regenerating situ atac-seq rna-seq motif

• Clinico-pathogenetic findings and management of chondrodystrophic myotonia (Schwartz-Jampel syndrome): a case report.

  PMID 12839625 · PMC166146 · BMC neurology · 2003 · 8 claims · 7 setups

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  The patient is a compound heterozygote with a different splicing mutation in each Perlecan allele, causing a significant reduction in production of the normal (wild-type) protein.

  8-year-old muscle lower skeletal molecular immunostaining electromyogram

• Inferring combinatorial regulation of transcription in silico.

  PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

  upstream monocytes same tfbs microarray permutation

• Slowly progressive encephalopathy with hearing loss due to a mutation in the mtDNA tRNA(Leu(CUN)) gene.

  PMID 20022607 · PMC3891822 · Journal of the neurological sciences · 2010 · 8 claims · 7 setups

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  The heteroplasmic m.12276G>A mtDNA tRNA Leu(CUN) mutation causes a childhood-onset, slowly progressive encephalopathy with ataxia, cognitive impairment, dyspraxia, and sensorineural hearing loss

  skeletal muscle genomic individual histochemistry biochemical direct

• Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium.

  PMID 17407598 · PMC1852558 · BMC genomics · 2007 · 8 claims · 7 setups

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  Global protein expression profiles of cultured intestinal epithelial cell lines differ from those of intestinal epithelial scrapings in vivo

  caco-2 ht-29 hep muscle 2-d 2-de principal

• Transcription-terminating mutation in telethonin causing autosomal recessive muscular dystrophy type 2G in a European patient.

  PMID 18948002 · PMC2592511 · Neuromuscular disorders : NMD · 2008 · 7 claims · 7 setups

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  The patient carries a homozygous Trp25X (TGG→TGA) mutation in TCAP causing premature termination of translation/transcription and complete telethonin deficiency.

  pelvis skeletal muscle genomic muscle histology electron

• Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

  PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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  A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

  lsl-krasg12d soft combined mfh microarray gene oncogenic

• Novel CLCN1 mutations and clinical features of Korean patients with myotonia congenita.

  PMID 19949657 · PMC2775849 · Journal of Korean medical science · 2009 · 7 claims · 8 setups

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  Sequencing of CLCN1 in 10 unrelated Korean MC patients identified nine different point mutations, six of which are novel (p.M128I, p.S189C, p.M373L, p.P480S, p.G523D, p.M609K).

  genomic frozen skeletal korean direct rt-pcr-based pcr-restriction

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells are largely distinct, non-overlapping populations across murine and human aging tissues, with only rare double-positive cells

  young spleen brain single-cell mass velocity

• Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

  PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

  longissimus muscle snps pig h3k27ac strand-specific starr-seq

• Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.

  PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 8 claims · 6 setups

  Has reproduction · 93

  Age-related decrease in transcriptome conservation (ADICT) is commonly found in ageing tissues of nonmammalian species (chicken brain, killifish liver and skin, fruit fly brain).

  gallus nothobranchius drosophila heterocephalus bulk single-cell

• Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis).

  PMID 40361012 · PMC12070547 · BMC genomics · 2025 · 6 claims · 8 setups

  Has reproduction · 80

  A core set of 74 differentially expressed genes responds to heat stress in at least seven of nine abalone transcriptomic studies, constituting a conserved core heat-stress response across the genus Haliotis.

  discus diversicolor fulgens laevigata bulk